Troubles in Paradise is a massive review of the creationism/ID movement, its people, and its arguments, along with a similarly massive review of relevant scientific evidence and literature. TIP primarily covers the movement up to about 2004, which of course was just about the peak of the ID movement, leading up to the 2005 Kitzmiller v. Dover case.

I think it is extremely valuable to the pro-science community to have such a historical review available: the ID movement actively tries to conceal what it was saying pre-Kitzmiller, and of course the “intelligent design” label itself was an attempt to disguise connections to creation science. (And, “creation science,” particularly the whitewashed version put forward for the Edwards v. Aguillard case, was its own attempt at obscuring connections to religious fundamentalism.) (On this, see especially: Matzke, N. (2009), “But Isn’t It Creationism? The beginnings of ‘intelligent design’ and Of Pandas and People in the midst of the Arkansas and Louisiana litigation.” In: But Is It Science?: The Philosophical Question in the Creation/Evolution Controversy, Updated Edition, eds. Pennock & Ruse, Prometheus Books, 377-413; google Scholar)

Today in 2015, it is not uncommon for commentators new to the creationism/ID debate to start producing writings almost totally ignorant of the history of the issue. Hopefully Downard’s effort will help correct this problem, and will serve as a resource that science fans can link to and cite.

Troubles in Paradise is really several books’ worth of work, so if you’ve ever gone to the bookstore and bought a science book, please think about making a similar donation so that Downard can continue his efforts.

Welcome to TIP, a new open access resource for defenders of sound science who get really unsettled by the claims of antievolutionists (be they Young Earth Creationists or the newer brand of Intelligent Design) but may not have all the best science information ready to drop on their claims.

The TIP files (all in pdf format) cover all aspects of antievolutionism (from paleontology and biology to the social and political ramifications of antievolutionism as they play out in schoolrooms and school boards or in state legislatures, Congress, or even candidates for President.

The Old TIP files form the base of the project, drawing on over 5500 sources, and step by step I am updating that material with a much larger set of newer data (over 36,000 sources and counting, including over 14,000 technical science sources aimed at claims popping up in over 6000 antievolutionist works) to keep TIP constantly current. The new modules also have an index to help locating all specific topics and people covered.

There are more pdfs & offsite web links in Other Stuff, including the 3ME illustrated guide to the Cambrian Explosion, and the origin of birds and mammals, the perfect heavy brick to lob at antievolutionists who make the mistake of claiming “there’s no evidence for macroevolution.” 3ME not only shows how wrong that is, it also pulls back the curtain to see just how antievolutionists manage to evade all that evidence (not a pretty picture, but has to be done).

Check out all the material here on TIP, all open access to download and share freely with anyone you think needs evens stronger evidence to counter the claims of antievolutionists.

Anyone who relies on the Supreme Court to guarantee that creationism will not be taught in public school or that the Ark Park’s threatened lawsuit will necessarily fail might want to read an article by Erwin Chemerinsky in the January 1 issue of The Washington Spectator. In that article, which I take to be a longish abstract of his book, Chemerinsky argues that the Court has generally not lived up to its “lofty expectations” and indeed has more often “upheld discrimination and even egregious violations of basic liberties.” The Chemerinsky article does not appear on the Spectator website, so I will abstract it very briefly below the fold.
———-Update, January 5, 2015. The article is now available here, so you may read it for yourself and not take my word for what Chemerinsky says.
———-

On August 14, William Dembski spoke at the Computations in Science Seminar at the University of Chicago. Was this a sign that Dembski’s arguments for intelligent design were being taken seriously by computational scientists? Did he present new evidence? There was no new evidence, and the invitation seems to have come from Dembski’s Ph.D. advisor Leo Kadanoff. I wasn’t present, and you probably weren’t either, but fortunately we can all
view the seminar, as a video of it has been posted here on Youtube.

It turns out that Dembski’s current argument is based on two of his previous
papers with Robert Marks (available
here
and
here) so the arguments are not new. They involve considering
a simple model of evolution in which we have all possible genotypes, each of
which has a fitness. It’s a simple model
of evolution moving uphill on a fitness surface. Dembski and Marks argue that
substantial evolutionary progress can only be made if the fitness
surface is smooth enough, and that setting up a smooth enough fitness
surface requires a Designer.

Briefly, here’s why I find their argument unconvincing:

They conside all possible ways that the set of fitnesses can be
assigned to the set of genotypes. Almost all of these look like
random assigments of fitnesses to genotypes.

Given that there is a random association of genotypes and
fitnesses, Dembski is right to assert that it is very hard to make much
progress in evolution. The fitness surface is a “white noise”
surface that has a vast number of very
sharp peaks. Evolution will make progress only until it climbs the nearest
peak, and then it will stall. But …

That is a very bad model for real biology, because in that case one
mutation is as bad for you as changing all sites in your genome at the same
time!

Also, in such a model all parts of the genome interact extremely strongly,
much more than they do in real organisms.

Dembski and Marks acknowledge that if the fitness surface is smoother than that, progress can be made.

They then argue that choosing a smooth enough fitness surface out of all possible ways of associating the fitnesses with the genotypes requires a Designer.

But I argue that the ordinary laws of physics actually imply a surface a lot smoother than a random map of sequences to fitnesses. In particular if gene expression is separated in time and space, the genes are much less likely to interact strongly, and the fitness surface will be much smoother
than the “white noise” surface.

Dembski and Marks implicitly acknowledge, though perhaps just for the sake of argument, that natural selection can create adaptation. Their
argument does not require design to occur once the fitness surface is
chosen. It is thus a Theistic Evolution argument rather than one that
argues for Design Intervention.

That’s a lot of argument to bite off in one chew. Let’s go into more
detail below the fold …

8. New perspective.
I think there are several different varieties of creationism activists. Some are obsessed with the presumed negative effects of evolution and secular humanism. Some are driven by suspicion for science and the certainty that a conspiracy must be afoot. Some use creationist apologetics to make themselves feel smarter and better-informed than the general public. Some are genuinely interested in science and want to know the truth.

I’d be lying if I said my motivations for arguing creationism were firmly in the last camp. I wasn’t much of a conspiracy theorist, but I certainly believed that there were inevitable negative consequences from the acceptance of evolution. I was definitely stuck-up about my “special” expertise. But deep down, I really did want to know the truth about the world. I loved being right, but I loved learning new things more.

The final set of creationist misconceptions about evolution surrounds its supposed religious, moral, and ethical implications. These objections prove difficult to address, simply because they have little or no objective basis and are almost purely philosophical or religious. This section will concentrate mostly on explaining the relationships and connections between these arguments, as systematically refuting them would delve deep into philosophy and theology and is far beyond the scope of a single post.

Perhaps one of the clearest and most obvious confirmations of evolution is the convergence between the evolutionary paths of descent determined by fossil evidence and the phylogenetic tree generated by algorithms analyzing genetic information. Because the tree of universal common descent is real, not invented, it leaves the same fingerprint in every part of nature that life touches. Matching trees can be found in global fossil distribution, in analysis of skeletal morphologies, in chromosome length, count, and banding, and in numerous common genetic sequences.

Not every genetic sequence yields a perfect branching tree. Evolutionary theory would not predict perfect branching trees, because random mutations scramble the relationships over time. Even though mutations provide the variation needed for diversification, their accumulation throughout that diversification can eventually obscure the evidence needed to reconstruct those relationships.

Most creationists believe that the theory of evolution was developed out of an ideological commitment to explaining life apart from God. Explanations of the history of evolutionary theory often point out personal struggles in the lives of prominent scientists – Darwin most often, of course – in support of this belief. “Secular scientists wanted a way of explaining a world that didn’t require God, so they invented this ridiculous theory.” To creationists, this foundation offers an easy way of dismissing all the theoretical and observational bases of evolution. If evolution is just wishful thinking born of anti-theistic extremism, then all the “evidence” is reduced to ad hoc speculation.

Because of this misconception, creationists rarely understand the actual history of how geology, paleontology, and biology built upon each other to provide us with our understanding of the world. Mainstream geology emerged significantly ahead of Darwin’s work; many early geologists were Christians. Studying the distribution of rock layers around the globe allowed geologists to construct a complete geologic column and begin appreciating the incredible amount of time the column represents. Moreover, the regular progression of extinct species fossilized throughout the geologic column had been well-catalogued.

One of the most common and most frustrating creationist objections to evolution is the claim that there are no “missing links” or “transitional fossils” required by evolution. This claim is made without qualification, particularly in presentations to lay or church audiences. As unthinkable as it might seem, creationists really do believe that transitional fossils simply do not exist. On this basis, they conclude that evolution must be false.

They maintain this completely erroneous view by consistently misrepresenting what a transitional fossil actually is. Creationists don’t deny that Archaeopteryx, Pakicetus, Tiktaalik, Australopithecus, and similar prominent examples of transitional fossils exist; they rather argue that these are not “true” transitional fossils.

I’ve a brief new article in the new Skeptical Inquirer (July/August 2014) regarding Casey Luskin’s botched attack on the second episode of Cosmos. Here it follows - your comments are welcomed.

Fox TV’s Seth McFarlane has joined with astrophysicist Neil deGrasse Tyson and Ann Druyan, Carl Sagan’s widow and collaborator, to continue Sagan’s marvelous Cosmos series of decades ago. The new series is a splendid blend of homage to Sagan’s original one with dazzling new graphics–and new discoveries.

The second episode of the series, first broadcast March 16, 2014, covered
evolution and natural selection. (Link) As expected, creationists were furious. The
main promoter of “intelligent design,” Seattle’s Discovery Institute, has run several anti-Cosmos blogs on its Evolution News and Views (ENV) website.

In their zeal to attack Tyson and the Cosmos series, however, the Discovery Institute has created a stunning example of the straw man logical fallacy. This fallacy is so named because it involves attacking one’s opponent not by an honest dissection of his or her actual views but by attacking a caricature, a distorted misrepresentation of those views. The Discovery Institute’s attack on the evolution episode of Cosmos was a particularly egregious example of this fallacy–a straw man for the ages, as it were.

Creationists often conceptualize evolution as something which is purely vertical: successive changes from parent to child to grandchild to great-grandchild accumulating over time. They can hardly be faulted for this misconception, because this view seems to be shared by the general public and even reinforced by the sometimes-imprecise explanations and depictions of evolution by museums and science educators.

Evolutionary adaptation, however, does not happen in a straight line from parent to child. Rather, adaptation takes place throughout a population as different genetic sequences spread outward from parents to all their offspring and are recombined and reshuffled in many different individuals each successive generation. Evolution is wibbly-wobbly, timey-wimey stuff. It is the combination of changing genetic material across an entire population that makes major evolutionary adaptation possible; without this constant mixing and recombination from the entire population, evolution would grind almost to a halt. Evolution is a phenomenon that functions not at the level of the individual, nor at the level of individual lineages, but across the entire population within the species (Figure 1).

Figure 1. This hypothetical example depicts evolutionary change as an emergent property of the entire population. Both the “ABC” combinations (in shades of blue) and the “XYZ” combinations (in shades of red) offer a survival advantage and are passed on, while combinations of the two (shown in shades of purple) are detrimental and are removed from the population. No specific mutation order is required; as long as the selection pressure remains steady, the mutations accumulate together (essentially “finding” each other) and two separate genotypes emerge.

The majority of modern creation science freely admits the existence of biological variation, adaptation, and speciation. Indeed, the recent-creation model – particularly the belief that all extant life descended from a small group of “kinds” present on Noah’s Ark which diversified into all families on Earth after a global flood – requires enormous adaptive variation and near-constant speciation. Creationists estimate that fewer than 10,000 pairs of land-dwelling, air-breathing animals on the Ark diversified to represent all families alive today. There are around 6.5 million land-dwelling species today, so millions of speciation events would have needed to take place over the past 44 centuries since their global flood.

In this short series, David MacMillan explains how misinformation and misconceptions allow creationists to maintain their beliefs even in the face of overwhelming evidence to the contrary. A former creationist blogger and writer, Mr. MacMillan earned his BS degree in physics from the University of North Alabama and now works as a technical writer when he isn’�t frequenting the PT comment boards. Since leaving creationism, he has written several columns discussing the public dialogue between creation and evolution. This series will outline the core beliefs creationists use as the basis for their reasoning while pointing out the challenges faced in re-educating against creationist misconceptions.

Note added July 16, approx. 4:30 p.m.: I have added links to all the articles subsequent to this one at the bottom of the page.

1. Introduction and overview: Philosophy of pseudoscience

During my tenure as an active young-earth creationist, I never once heard other creationists accurately describe what evolutionary theory is or how it is supposed to work. Nor did I understand it myself. Creationists often seem familiar with a lot of scientific terminology, but their understanding is filled with gross misinformation. Thus, a host of misconceptions is believed and taught throughout creationist circles, making it almost impossible for actual evidence to really sink in.

There are plenty of comprehensive lists of creationist claims with exhaustive refutations, such as the TalkOrigins archive. Rather than try to replicate those, I will attempt to explain why creationist claims persist in the face of contrary evidence, even when individuals are otherwise well-educated. To do so, I’m going to go over the major areas where creationists get the science itself completely wrong. My list doesn’t represent all such misconceptions, of course. These are the misconceptions I personally recall hearing or using myself. I’ve chosen not to provide specific examples of each misconception from the creationist literature, though they are all easy to find. Citations for my explanations can be found online by anyone who wants to see them; this series is not about any particular facts so much as it’s about how false beliefs are used to support false conclusions.

Apparently not at Bryan College (yes, that Bryan) in Dayton, Tennessee (yes, that Dayton), according to an article in yesterday’s Times. The college, founded in 1930, requires faculty to sign a statement agreeing to certain reactionary views on creation and evolution, including, “The origin of man was by fiat of God,” according to the article by Alan Blinder.

Several months ago, the college added a “clarification” to the effect that Adam and Eve “are historical persons created by God in a special formative act, and not from previously existing life-forms,” according to Blinder. There is a ray of hope, however: “Hundreds” of students out of a student body of approximately 700 petitioned the trustees and opposed the clarification. Two faculty members filed a lawsuit, arguing that the college charter does not permit the trustees to change the statement of belief. A biology professor, Brian Eisenback, called the clarification “scientifically untenable” and accepted a position at another Christian liberal arts college in Tennessee.

Others argue that a college is not a church and should not prescribe doctrine, but the trustees are determined to enforce their policy. The president, Stephen D. Livesay, noted

But this is Bryan College, and this is something that’s important to us. It’s in our DNA… [my italics].

I trust that I am not the only one who finds that allusion uproariously funny.

This novel by Lauren Grodstein is about Andy, a once promising biology professor now languishing in the tenure-track of a third-rank university in New Jersey. Andy teaches a course nicknamed There Is No God, whose principles are these:

1: Evolution is the explanation for everything

2: Darwin is right

3: And people who don’t believe Darwin are wrong

That is about right, at least to first order and as far as biology is concerned, but naturally such an explicit statement is bound to attract attention. Indeed, it attracts the attention of Lionel, a Campus Crusade type who has received permission to take Andy’s course for a second time in order to make a case against Andy. More importantly, as it turns out, Lionel sets Andy up by encouraging another student, Melissa, to ask Andy to mentor her in a reading course on intelligent-design creationism. Andy resists but finally gives in, with predictably dire consequences.

From the website of the Schilling School, “A Nationally Recognized K-12 [Charter] School for the Gifted in Cincinnati, Ohio”:

Dr. Michael Behe to present at Schilling. Mark your calendar for Sunday, April 6th from 7:00 pm - 9:00 pm to hear him present, “ Feeling left out by the Ham-Nye Debate? The Reasonable Middle Ground of Intelligent Design.” Call 489-8940 for ticket prices and group rates.

Congratulations to our 2014 U.C. Science Fair winners. All of our students won a cash prize. Two of our students Salma and Daniel have been invited to participate at the state science fair in Columbus next month. Good luck to the both of them!

Well, AiG’s Ken Ham has seen the movie “Noah” starring Russell Crowe, and boy, is he steamed!

Friends, I just arrived home after seeing the Hollywood (Paramount) movie NOAH tonight. It is MUCH much worse than I thought it would be. Much worse.

The Director of the movie, Darren Aronofsky has been quoted in the media as saying NOAH is ‘the least biblical biblical film ever made’, I agree wholeheartedly with him.

I am disgusted. I am going to come right out and say it-it is disgusting and evil-paganism! Do you really want your family to see a pagan movie the has Noah as some psychopath who says if his daughter-in-law’s baby is a girl, he will kill it as soon as it’s born. And then when two girls are born, bloodstained Noah (the man the Bible calls righteous Noah-Genesis 7:1), brings a knife down to one of the baby’s heads to kill it and at the last minute doesn’t do it-and then a bit later says he failed because he didn’t kill the babies. How can we recommend this movie and then speak against abortion! Psychopathic Noah sees humans as a blight on the planet and wants to rid the world of people.

People have been sending me this, so I might as well blog it. In February 2014, Svante P��bo, who led the Neanderthal genome project, published a popular book on the sequencing of the Neanderthal genome, and reactions to it.

I haven’t yet read the book, although I’m sure it’s great, based on talks I have seen by P��bo. However, there is one passage that PT readers may find particularly interesting:

There were many others who were interested in the Neanderthal genome – perhaps most surprisingly, some fundamentalist Christians in the United States. A few months after our paper appeared, I met Nicholas J. Matzke, a doctoral candidate at the Center for Theoretical Evolutionary Genomics at UC Berkeley. Unbeknownst to me and the other authors, our paper had apparently caused quite a flurry of discussion in the creationist community. Nick explained to me that creationists come in two varieties. First, there are “young-earth creationists,” who believe that the earth, the heavens, and all life were created by direct acts of God sometime between 5,700 and 10,000 years ago. They tend to consider Neanderthals as “fully human,” sometimes saying they were another, now extinct “race” that was scattered after the fall of the Tower of Babel. As a consequence, young-earth creationists had no problem with our finding that Neanderthals and modern humans had mixed. Then there are “old-earth creationists,” who accept that the earth is old but reject evolution by natural, nondivine means. One major old-earth ministry is “Reasons to Believe,” headed by a Hugh Ross. He believes that modern humans were specially created around 50,000 years ago and that Neanderthals weren’t humans, but animals. Ross and other old-earth creationists didn’t like the finding that Neanderthals and modern humans had mixed. Nick sent me a transcript from a radio show in which he [meaning Hugh Ross] commented on our work, saying interbreeding was predictable “because the story of Genesis is early humanity getting into exceptionally wicked behavior practices,” and that God may have had to “forcibly scatter humanity over the face of the Earth” to stop this kind of interbreeding, which he compared to “animal bestiality.”

Clearly our paper was reaching a broader audience than we had ever imagined.

A Crystal disco ball to celebrate the crystal anniversary of the Disco. ‘tute’s entry into the creationism business.

Fifteen years ago yesterday, a mail clerk in Seattle was handed a document to copy. As the Seattle Weeklyreported, the packet was labeled “TOP SECRET” and “NOT FOR DISTRIBUTION,” and the cover sported an Illuminati-esque triangular design and a copy of Michelangelo’s “Creation of Adam.” The title: “The Wedge”; the author: a newly-created division of the conservative Discovery Institute, the Center for the Renewal of Science and Culture (CRSC). Later, the Center would drop “renewal” from its title to escape the religious reference, and also switched its logo from the Creation of Adam to a picture of God creating DNA, then to a more secular galactic nebula, and now a mashup of Leonardo’s Vitruvian man and a DNA strand.

The Wedge Document, as the packet came to be known, laid out a bold plan by which the Center would “re-open the case for a broadly theistic understanding of nature,” and “reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.” From its first sentence, the document proclaimed its sectarian goals, stating: “The proposition that human beings are created in the image of God is one of the bedrock principles on which Western civilization was built. Its influence can be detected in most, if not all, of the West’s greatest achievements, including representative democracy, human rights, free enterprise, and progress in the arts and sciences.”

Everyone seems to be talking about the Bill Nye vs. Ken Ham debate which is occurring in a few hours. I’m not going to watch it, at least not immediately. I’m not 100% against debating creationists, but I do think science-defenders should try to not give the contest away before it even starts.

For a long time I’ve been developing a list in my head of what scientists and science educators should think about even before they even agree to appear in a debate. Bill Nye made all of these mistakes at once, and therefore, even if he and his bow-tie have the best day of their lives, he’s lost on a lot of fronts already. All Ken Ham has to do to win is not break down in tears and admit he’s based his life on a horrible mistake.

Therefore, here are my…

TEN (well, 7 & counting) COMMANDMENTS THOU SHALT THINK ABOUT, AND RESOLVE, BEFORE YOU EVEN AGREE TO DEBATE A CREATIONIST